X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasDatastore.java;h=2632b2a367267ef219efbf77cc5292b70d464fa2;hb=ff385fde554b8fe517dbb734ca687ef7552f2350;hp=2f43f031a9341c78843872c9353961ff415449fb;hpb=4d2e0d36506302cc00677527725bcccbdf27d766;p=jalview.git diff --git a/src/jalview/io/VamsasDatastore.java b/src/jalview/io/VamsasDatastore.java index 2f43f03..2632b2a 100755 --- a/src/jalview/io/VamsasDatastore.java +++ b/src/jalview/io/VamsasDatastore.java @@ -1,1552 +1,1900 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ - -package jalview.io; - -import org.vamsas.client.Vobject; -import org.vamsas.client.VorbaId; -import org.vamsas.objects.core.*; -import org.vamsas.objects.utils.DocumentStuff; -import org.vamsas.test.simpleclient.ClientDoc; - -import jalview.bin.Cache; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.AlignmentView; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceI; -import jalview.gui.*; - -import java.io.*; -import java.util.HashMap; -import java.util.HashSet; -import java.util.Hashtable; -import java.util.IdentityHashMap; -import java.util.Vector; -import java.util.jar.*; -import org.exolab.castor.xml.*; -import org.exolab.castor.mapping.Mapping; - -/* - * - * static { - * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty( - * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); } - * - */ - -public class VamsasDatastore { - Entry provEntry = null; - - // AlignViewport av; - - org.exolab.castor.types.Date date = new org.exolab.castor.types.Date( - new java.util.Date()); - - ClientDoc cdoc; - - Hashtable vobj2jv; - - IdentityHashMap jv2vobj; - - public VamsasDatastore(ClientDoc cdoc, Hashtable vobj2jv, - IdentityHashMap jv2vobj, Entry provEntry) { - this.cdoc = cdoc; - this.vobj2jv = vobj2jv; - this.jv2vobj = jv2vobj; - this.provEntry = provEntry; - } - - /* - * public void storeJalview(String file, AlignFrame af) { try { // 1. Load the - * mapping information from the file Mapping map = new - * Mapping(getClass().getClassLoader()); java.net.URL url = - * getClass().getResource("/jalview_mapping.xml"); map.loadMapping(url); // 2. - * Unmarshal the data // Unmarshaller unmar = new Unmarshaller(); - * //unmar.setIgnoreExtraElements(true); //unmar.setMapping(map); // uni = - * (UniprotFile) unmar.unmarshal(new FileReader(file)); // 3. marshal the data - * with the total price back and print the XML in the console Marshaller - * marshaller = new Marshaller( new FileWriter(file) ); - * - * marshaller.setMapping(map); marshaller.marshal(af); } catch (Exception e) { - * e.printStackTrace(); } } - * - * - */ - /** - * @return the Vobject bound to Jalview datamodel object - */ - protected Vobject getjv2vObj(Object jvobj) { - if (jv2vobj.containsKey(jvobj)) - return cdoc.getObject((VorbaId) jv2vobj.get(jvobj)); - return null; - } - - /** - * - * @param vobj - * @return Jalview datamodel object bound to the vamsas document object - */ - protected Object getvObj2jv(org.vamsas.client.Vobject vobj) { - VorbaId id = vobj.getVorbaId(); - if (id == null) - { - id = cdoc.registerObject(vobj); - Cache.log - .debug("Registering new object and returning null for getvObj2jv"); - return null; - } - if (vobj2jv.containsKey(vobj.getVorbaId())) - return vobj2jv.get(vobj.getVorbaId()); - return null; - } - - protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj) { - VorbaId id = vobj.getVorbaId(); - if (id == null) - { - id = cdoc.registerObject(vobj); - if (id==null || vobj.getVorbaId()==null) - Cache.log.error("Failed to get id for "+(vobj.isRegisterable() ? "registerable" : "unregisterable") +" object "+vobj); - } - - if (vobj2jv.containsKey(vobj.getVorbaId()) && !((VorbaId)vobj2jv.get(vobj.getVorbaId())).equals(jvobj)) { - Cache.log.debug("Warning? Overwriting existing vamsas id binding for "+vobj.getVorbaId(), new Exception("Overwriting vamsas id binding.")); - } - else if (jv2vobj.containsKey(jvobj) && !((VorbaId)jv2vobj.get(jvobj)).equals(vobj.getVorbaId())) - { - Cache.log.debug("Warning? Overwriting existing jalview object binding for "+jvobj, new Exception("Overwriting jalview object binding.")); - } - /* Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id " +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+" already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to bindjvvobj")); - }*/ - // we just update the hash's regardless! - vobj2jv.put(vobj.getVorbaId(), jvobj); - // JBPNote - better implementing a hybrid invertible hash. - jv2vobj.put(jvobj, vobj.getVorbaId()); - } - - /** - * put the alignment viewed by AlignViewport into cdoc. - * - * @param av alignViewport to be stored - * @param aFtitle title for alignment - */ - public void storeVAMSAS(AlignViewport av, String aFtitle) { - try - { - jalview.datamodel.AlignmentI jal = av.getAlignment(); - boolean nw = false; - VAMSAS root = null; // will be resolved based on Dataset Parent. - // ///////////////////////////////////////// - // SAVE THE DATASET - if (jal.getDataset() == null) - { - Cache.log.warn("Creating new dataset for an alignment."); - jal.setDataset(null); - } - DataSet dataset = (DataSet) getjv2vObj(jal.getDataset()); - if (dataset == null) - { - root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying. - dataset = new DataSet(); - root.addDataSet(dataset); - bindjvvobj(jal.getDataset(), dataset); - dataset.setProvenance(dummyProvenance()); - dataset.getProvenance().addEntry(provEntry); - nw = true; - } - else - { - root = (VAMSAS) dataset.getV_parent(); - } - // update dataset - Sequence sequence; - DbRef dbref; - // set new dataset and alignment sequences based on alignment Nucleotide - // flag. - // this *will* break when alignment contains both nucleotide and amino - // acid sequences. - String dict = jal.isNucleotide() ? org.vamsas.objects.utils.SymbolDictionary.STANDARD_NA - : org.vamsas.objects.utils.SymbolDictionary.STANDARD_AA; - for (int i = 0; i < jal.getHeight(); i++) - { - SequenceI sq = jal.getSequenceAt(i).getDatasetSequence(); // only insert - // referenced - // sequences - // to dataset. - sequence = (Sequence) getjv2vObj(sq); - if (sequence == null) - { - sequence = new Sequence(); - bindjvvobj(sq, sequence); - sq.setVamsasId(sequence.getVorbaId().getId()); - sequence.setSequence(sq.getSequenceAsString()); - sequence.setDictionary(dict); - sequence.setName(jal.getDataset().getSequenceAt(i).getName()); - sequence.setStart(jal.getDataset().getSequenceAt(i).getStart()); - sequence.setEnd(jal.getDataset().getSequenceAt(i).getEnd()); - dataset.addSequence(sequence); - } - else - { - // verify principal attributes. and update any new - // features/references. - System.out.println("update dataset sequence object."); - } - if (sq.getSequenceFeatures() != null) - { - int sfSize = sq.getSequenceFeatures().length; - - for (int sf = 0; sf < sfSize; sf++) - { - jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) sq - .getSequenceFeatures()[sf]; - - DataSetAnnotations dsa = (DataSetAnnotations) getjv2vObj(feature); - if (dsa == null) - { - dsa = (DataSetAnnotations) getDSAnnotationFromJalview( - new DataSetAnnotations(), feature); - if (dsa.getProvenance() == null) - { - dsa.setProvenance(new Provenance()); - } - addProvenance(dsa.getProvenance(), "created"); // JBPNote - need - // to update - dsa.setSeqRef(sequence); - bindjvvobj(feature, dsa); - dataset.addDataSetAnnotations(dsa); - } - else - { - // todo: verify and update dataset annotations for sequence - System.out.println("update dataset sequence annotations."); - } - } - } - - if (sq.getDBRef() != null) - { - DBRefEntry[] entries = sq.getDBRef(); - jalview.datamodel.DBRefEntry dbentry; - for (int db = 0; db < entries.length; db++) - { - dbentry = entries[db]; - dbref = (DbRef) getjv2vObj(dbentry); - if (dbref == null) - { - dbref = new DbRef(); - bindjvvobj(dbentry, dbref); - dbref.setAccessionId(dbentry.getAccessionId()); - dbref.setSource(dbentry.getSource()); - dbref.setVersion(dbentry.getVersion()); - /* - * TODO: Maps are not yet supported by Jalview. Map vMap = new - * Map(); vMap.set dbref.addMap(vMap); - */ - sequence.addDbRef(dbref); - } - else - { - // TODO: verify and update dbrefs in vamsas document - // there will be trouble when a dataset sequence is modified to - // contain more residues than were originally referenced - we must - // then make a number of dataset sequence entries - System.out - .println("update dataset sequence database references."); - } - } - - } - } - // dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance())); - // //////////////////////////////////////////// - - // //////////////////////////////////////////// - // Save the Alignments - - Alignment alignment = (Alignment) getjv2vObj(av); // this is so we can get the alignviewport back - if (alignment == null) - { - alignment = new Alignment(); - bindjvvobj(av, alignment); - if (alignment.getProvenance() == null) - alignment.setProvenance(new Provenance()); - addProvenance(alignment.getProvenance(), "added"); // TODO: insert some - // sensible source - // here - dataset.addAlignment(alignment); - { - Property title = new Property(); - title.setName("jalview:AlTitle"); - title.setType("string"); - title.setContent(aFtitle); - alignment.addProperty(title); - } - alignment.setGapChar(String.valueOf(av.getGapCharacter())); - AlignmentSequence alseq = null; - for (int i = 0; i < jal.getHeight(); i++) - { - alseq = new AlignmentSequence(); - // TODO: VAMSAS: translate lowercase symbols to annotation ? - alseq.setSequence(jal.getSequenceAt(i).getSequenceAsString()); - alseq.setName(jal.getSequenceAt(i).getName()); - alseq.setStart(jal.getSequenceAt(i).getStart()); - alseq.setEnd(jal.getSequenceAt(i).getEnd()); - alseq.setRefid(getjv2vObj(jal.getSequenceAt(i).getDatasetSequence())); - alignment.addAlignmentSequence(alseq); - bindjvvobj(jal.getSequenceAt(i), alseq); - } - } - else - { - // todo: verify and update mutable alignment props. - if (alignment.getModifiable()) - { - System.out.println("update alignment in document."); - } - else - { - System.out - .println("update edited alignment to new alignment in document."); - } - } - // //////////////////////////////////////////// - // SAVE Alignment Sequence Features - for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++) - { - AlignmentSequence valseq; - SequenceI alseq = (SequenceI) getvObj2jv(valseq = alignment - .getAlignmentSequence(i)); - if (alseq != null && alseq.getSequenceFeatures() != null) - { - jalview.datamodel.SequenceFeature[] features = alseq - .getSequenceFeatures(); - for (int f = 0; f < features.length; f++) - { - if (features[f] != null) - { - AlignmentSequenceAnnotation valseqf = (AlignmentSequenceAnnotation) getjv2vObj(features[i]); - if (valseqf == null) - { - - valseqf = (AlignmentSequenceAnnotation) getDSAnnotationFromJalview( - new AlignmentSequenceAnnotation(), features[i]); - if (valseqf.getProvenance() == null) - { - valseqf.setProvenance(new Provenance()); - } - addProvenance(valseqf.getProvenance(), "created"); // JBPNote - - // need to - // update - bindjvvobj(features[i], valseqf); - valseq.addAlignmentSequenceAnnotation(valseqf); - } - } - - } - } - } - - // //////////////////////////////////////////// - // SAVE ANNOTATIONS - if (jal.getAlignmentAnnotation() != null) - { - jalview.datamodel.AlignmentAnnotation[] aa = jal - .getAlignmentAnnotation(); - java.util.HashMap AlSeqMaps = new HashMap(); // stores int maps from - // alignment columns to - // sequence positions. - for (int i = 0; i < aa.length; i++) - { - if (aa[i] == null || isJalviewOnly(aa[i])) - { - continue; - } - if (aa[i].sequenceRef != null) - { - org.vamsas.objects.core.AlignmentSequence alsref = (org.vamsas.objects.core.AlignmentSequence) getjv2vObj(aa[i].sequenceRef); - org.vamsas.objects.core.AlignmentSequenceAnnotation an = (org.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(aa[i]); - int[] gapMap = null; - if (AlSeqMaps.containsKey(aa[i].sequenceRef)) - { - gapMap = (int[]) AlSeqMaps.get(aa[i].sequenceRef); - } - else - { - gapMap = new int[aa[i].sequenceRef.getLength()]; - // map from alignment position to sequence position. - int[] sgapMap = aa[i].sequenceRef.gapMap(); - for (int a = 0; a < sgapMap.length; a++) - gapMap[sgapMap[a]] = a; - } - if (an == null) - { - an = new org.vamsas.objects.core.AlignmentSequenceAnnotation(); - Seg vSeg = new Seg(); - vSeg.setStart(1); - vSeg.setInclusive(true); - vSeg.setEnd(gapMap.length); - an.addSeg(vSeg); - an.setType("jalview:SecondaryStructurePrediction");// TODO: better fix this rough guess ;) - alsref.addAlignmentSequenceAnnotation(an); - bindjvvobj(aa[i],an); - // LATER: much of this is verbatim from the alignmentAnnotation - // method below. suggests refactoring to make rangeAnnotation the - // base class - an.setDescription(aa[i].description); - if (aa[i].graph > 0) - an.setGraph(true); // aa[i].graph); - else - an.setGraph(false); - an.setLabel(aa[i].label); - an.setProvenance(dummyProvenance()); // get provenance as user - // created, or jnet, or - // something else. - an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote - - // originally we - // were going to - // store - // graphGroup in - // the Jalview - // specific - // bits. - AnnotationElement ae; - for (int a = 0; a < aa[i].annotations.length; a++) - { - if (aa[i].annotations[a] == null) - { - continue; - } - - ae = new AnnotationElement(); - ae.setDescription(aa[i].annotations[a].description); - ae.addGlyph(new Glyph()); - ae.getGlyph(0) - .setContent(aa[i].annotations[a].displayCharacter); // assume - // jax-b - // takes - // care - // of - // utf8 - // translation - if (aa[i].graph!=jalview.datamodel.AlignmentAnnotation.NO_GRAPH) - ae.addValue(aa[i].annotations[a].value); - ae.setPosition(gapMap[a]+1); // position w.r.t. AlignmentSequence - // symbols - if (aa[i].annotations[a].secondaryStructure != ' ') - { - // we only write an annotation where it really exists. - Glyph ss = new Glyph(); - ss - .setDict(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE); - ss.setContent(String - .valueOf(aa[i].annotations[a].secondaryStructure)); - ae.addGlyph(ss); - } - an.addAnnotationElement(ae); - } - } - else - { - // update reference sequence Annotation - if (an.getModifiable()) - { - // verify existing alignment sequence annotation is up to date - System.out.println("update alignment sequence annotation."); - } - else - { - // verify existing alignment sequence annotation is up to date - System.out - .println("make new alignment sequence annotation if modification has happened."); - } - } - } - else - { - // add Alignment Annotation - org.vamsas.objects.core.AlignmentAnnotation an = (org.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(aa[i]); - if (an == null) - { - an = new org.vamsas.objects.core.AlignmentAnnotation(); - an.setType("jalview:AnnotationRow"); - an.setDescription(aa[i].description); - alignment.addAlignmentAnnotation(an); - Seg vSeg = new Seg(); - vSeg.setStart(1); - vSeg.setInclusive(true); - vSeg.setEnd(jal.getWidth()); - an.addSeg(vSeg); - if (aa[i].graph > 0) - an.setGraph(true); // aa[i].graph); - an.setLabel(aa[i].label); - an.setProvenance(dummyProvenance()); - if (aa[i].graph!=aa[i].NO_GRAPH) { - an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote - - // originally we - // were going to - // store - // graphGroup in - // the Jalview - // specific - // bits. - an.setGraph(true); - } else { - an.setGraph(false); - } - AnnotationElement ae; - - for (int a = 0; a < aa[i].annotations.length; a++) - { - if ((aa[i] == null) || (aa[i].annotations[a] == null)) - { - continue; - } - - ae = new AnnotationElement(); - ae.setDescription(aa[i].annotations[a].description); - ae.addGlyph(new Glyph()); - ae.getGlyph(0) - .setContent(aa[i].annotations[a].displayCharacter); // assume - // jax-b - // takes - // care - // of - // utf8 - // translation - ae.addValue(aa[i].annotations[a].value); - ae.setPosition(a+1); - if (aa[i].annotations[a].secondaryStructure != ' ') - { - Glyph ss = new Glyph(); - ss - .setDict(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE); - ss.setContent(String - .valueOf(aa[i].annotations[a].secondaryStructure)); - ae.addGlyph(ss); - } - an.addAnnotationElement(ae); - } - if (aa[i].editable) { - //an.addProperty(newProperty("jalview:editable", null, "true")); - an.setModifiable(true); - } - if (aa[i].graph!=jalview.datamodel.AlignmentAnnotation.NO_GRAPH) { - an.setGraph(true); - an.setGroup(Integer.toString(aa[i].graphGroup)); - an.addProperty(newProperty("jalview:graphType",null, - ((aa[i].graph==jalview.datamodel.AlignmentAnnotation.BAR_GRAPH) ? "BAR_GRAPH" : "LINE_GRAPH"))); - - /** and on and on.. - vProperty=new Property(); - vProperty.setName("jalview:graphThreshhold"); - vProperty.setContent(aa[i].threshold); - */ - - } - } - else - { - if (an.getModifiable()) - { - // verify annotation - update (perhaps) - Cache.log.info("update alignment sequence annotation. not yet implemented."); - } - else - { - // verify annotation - update (perhaps) - Cache.log.info("updated alignment sequence annotation added."); - } - } - } - } - } - // ///////////////////////////////////////////////////// - - // ////////////////////////////////////////////// - // /SAVE THE TREES - // ///////////////////////////////// - // FIND ANY ASSOCIATED TREES - if (Desktop.desktop != null) - { - javax.swing.JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - - for (int t = 0; t < frames.length; t++) - { - if (frames[t] instanceof TreePanel) - { - TreePanel tp = (TreePanel) frames[t]; - - if (tp.getAlignment() == jal) - { - Tree tree = (Tree) getjv2vObj(tp); - if (tree == null) - { - tree = new Tree(); - bindjvvobj(tp, tree); - tree.setTitle(tp.getTitle()); - Newick newick = new Newick(); - // TODO: translate sequenceI to leaf mappings to vamsas - // references - see tree specification in schema. - newick.setContent(tp.getTree().toString()); - newick.setTitle(tp.getTitle()); - tree.addNewick(newick); - tree.setProvenance(makeTreeProvenance(jal, tp)); - alignment.addTree(tree); - } - else - { - if (tree.getModifiable()) - { - // verify any changes. - System.out.println("Update tree in document."); - } - else - { - System.out - .println("Add modified tree as new tree in document."); - } - } - } - } - } - } - // Store Jalview specific stuff in the Jalview appData - // not implemented in the SimpleDoc interface. - } - - catch (Exception ex) - { - ex.printStackTrace(); - } - - } - - private Property newProperty(String name, String type, String content) { - Property vProperty=new Property(); - vProperty.setName(name); - if (type!=null) - vProperty.setType(type); - else - vProperty.setType("String"); - vProperty.setContent(content); - return vProperty; - } - - /** - * correctly create a RangeAnnotation from a jalview sequence feature - * - * @param dsa - * (typically DataSetAnnotations or AlignmentSequenceAnnotation) - * @param feature - * (the feature to be mapped from) - * @return - */ - private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa, - SequenceFeature feature) { - dsa.setType(feature.getType()); - Seg vSeg = new Seg(); - vSeg.setStart(feature.getBegin()); - vSeg.setEnd(feature.getEnd()); - vSeg.setInclusive(true); - dsa.addSeg(vSeg); - dsa.setDescription(feature.getDescription()); - dsa.setStatus(feature.getStatus()); - if (feature.links != null && feature.links.size() > 0) - { - for (int i = 0, iSize = feature.links.size(); i < iSize; i++) - { - String link = (String) feature.links.elementAt(i); - int sep = link.indexOf('|'); - if (sep > -1) - { - Link vLink = new Link(); - if (sep > 0) - vLink.setContent(link.substring(0, sep - 1)); - else - vLink.setContent(""); - vLink.setHref(link.substring(sep + 1)); // TODO: validate href. - dsa.addLink(vLink); - } - } - } - dsa.setGroup(feature.getFeatureGroup()); - return dsa; - } - - /** - * correctly creates provenance for trees calculated on an alignment by - * jalview. - * - * @param jal - * @param tp - * @return - */ - private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp) { - Provenance prov = new Provenance(); - prov.addEntry(new Entry()); - prov.getEntry(0).setAction("imported "+tp.getTitle()); - prov.getEntry(0).setUser(provEntry.getUser()); - prov.getEntry(0).setApp(provEntry.getApp()); - prov.getEntry(0).setDate(provEntry.getDate()); - if (tp.getTree().hasOriginalSequenceData()) - { - Input vInput = new Input(); - // LATER: check to see if tree input data is contained in this alignment - - // or just correctly resolve the tree's seqData to the correct alignment in - // the document. - // vInput.setObjRef(getjv2vObj(jal)); - vInput.setObjRef(getjv2vObj(tp.getViewPort())); - prov.getEntry(0).setAction("created "+tp.getTitle()); - prov.getEntry(0).addInput(vInput); - vInput.setName("jalview:seqdist"); - prov.getEntry(0).addParam(new Param()); - prov.getEntry(0).getParam(0).setName("treeType"); - prov.getEntry(0).getParam(0).setType("utf8"); - prov.getEntry(0).getParam(0).setContent("NJ"); - - int ranges[] = tp.getTree().seqData.getVisibleContigs(); - // VisibleContigs are with respect to alignment coordinates. Still need offsets - int start= tp.getTree().seqData.getAlignmentOrigin(); - for (int r = 0; r < ranges.length; r += 2) - { - Seg visSeg = new Seg(); - visSeg.setStart(1+start+ranges[r]); - visSeg.setEnd(start+ranges[r + 1]); - visSeg.setInclusive(true); - vInput.addSeg(visSeg); - } - } - return prov; - } - - /** - * - * @param tp - * @return Object[] { AlignmentView, AlignmentI - reference alignment for - * input } - */ - private Object[] recoverInputData(Provenance tp) { - for (int pe = 0; pe < tp.getEntryCount(); pe++) - { - if (tp.getEntry(pe).getInputCount() > 0) - { - if (tp.getEntry(pe).getInputCount() > 1) - Cache.log.warn("Ignoring additional input spec in provenance entry " - + tp.getEntry(pe).toString()); - // LATER: deal sensibly with multiple inputs. - Input vInput = tp.getEntry(pe).getInput(0); - if (vInput.getObjRef() instanceof org.vamsas.objects.core.Alignment) - { - // recover an AlignmentView for the input data - AlignViewport javport = (AlignViewport) getvObj2jv((org.vamsas.client.Vobject) vInput - .getObjRef()); - jalview.datamodel.AlignmentI jal = javport.getAlignment(); - jalview.datamodel.CigarArray view = javport.getAlignment().getCompactAlignment(); - int from = 1, to = jal.getWidth(); - int offset=0; // deleteRange modifies its frame of reference - for (int r = 0, s = vInput.getSegCount(); r < s; r++) - { - Seg visSeg = vInput.getSeg(r); - int se[] = getSegRange(visSeg,true); // jalview doesn't do bidirection alignments yet. - if (to < se[1]) - Cache.log.warn("Ignoring invalid segment in InputData spec."); - else - { - if (se[0] > from) - { - view.deleteRange(offset+from-1, offset+se[0] - 2); - offset-=se[0]-from; - } - from = se[1] + 1; - } - } - if (from < to) - { - view.deleteRange(offset+from-1, offset+to-1); // final deletion - TODO: check off by - // one for to - } - return new Object[] { new AlignmentView(view), jal }; - } - } - } - Cache.log.debug("Returning null for input data recovery from provenance."); - return null; - } - - /** - * get start0) { - DbRef [] dbref = vdseq.getDbRef(); - for(int db=0; db0) { - // LOAD ALIGNMENTS from DATASET - - for (int al=0,nal=dataset.getAlignmentCount(); al0) { - AlignmentSequenceAnnotation[] vasannot=valseq.getAlignmentSequenceAnnotation(); - for (int a=0; a0) { - // Add the new sequence annotations in to the alignment. - for (int an=0,anSize=newasAnnots.size(); an0) - { - org.vamsas.objects.core.AlignmentAnnotation[] an = alignment.getAlignmentAnnotation(); - - for (int j = 0; j < an.length; j++) - { - jalview.datamodel.AlignmentAnnotation jan=(jalview.datamodel.AlignmentAnnotation) getvObj2jv(an[j]); - if (jan!=null) { - // update or stay the same. - // TODO: should at least replace with a new one - otherwise things will break - // basically do this: - // jan.update(getjAlignmentAnnotation(jal, an[a])); // update from another annotation object in place. - - Cache.log.debug("update from vamsas alignment annotation to existing jalview alignment annotation."); - if (an[j].getModifiable()) { - // TODO: user defined annotation is totally mutable... - so load it up or throw away if locally edited. - Cache.log.info("NOT IMPLEMENTED - Recovering user-modifiable annotation - yet..."); - } - // TODO: compare annotation element rows - // TODO: compare props. - } else { - jan = getjAlignmentAnnotation(jal, an[j]); - jal.addAnnotation(jan); - bindjvvobj(jan, an[j]); - } - } - } - AlignFrame alignFrame; - if (av==null) { - Cache.log.debug("New alignframe for alignment "+alignment.getVorbaId()); - // /////////////////////////////// - // construct alignment view - alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - av=alignFrame.getViewport(); - String title = alignment.getProvenance().getEntry(alignment.getProvenance().getEntryCount()-1).getAction(); - if (alignment.getPropertyCount()>0) { - for (int p=0,pe=alignment.getPropertyCount(); p 0) - { - - for (int t = 0; t < alignment.getTreeCount(); t++) - { - Tree tree = alignment.getTree(t); - TreePanel tp=(TreePanel) getvObj2jv(tree); - if (tp!=null) { - Cache.log.info("Update from vamsas document to alignment associated tree not implemented yet."); - } else { - // make a new tree - Object[] idata = this.recoverInputData(tree.getProvenance()); - try { - AlignmentView inputData=null; - if (idata!=null && idata[0]!=null) - inputData = (AlignmentView) idata[0]; - tp = alignFrame.ShowNewickTree( - new jalview.io.NewickFile(tree.getNewick(0).getContent()), - tree.getNewick(0).getTitle()+" ("+tree.getVorbaId()+")",inputData, - 600, 500, - t * 20 + 50, t * 20 + 50); - bindjvvobj(tp, tree); - } catch (Exception e) { - Cache.log.warn("Problems parsing treefile '"+tree.getNewick(0).getContent()+"'",e); - } - } - } - } - - } - } - } - } - } - // bitfields - should be a template in j1.5 - private static int HASSECSTR=0; - private static int HASVALS=1; - private static int HASHPHOB=2; - private static int HASDC=3; - private static int HASDESCSTR=4; - private static int HASTWOSTATE=5; // not used yet. - /** - * parses the AnnotationElements - if they exist - into jalview.datamodel.Annotation[] rows - * Two annotation rows are made if there are distinct annotation for both at 'pos' and 'after pos' at any particular site. - * @param annotation - * @return { boolean[static int constants ], int[ae.length] - map to annotated object frame, jalview.datamodel.Annotation[], jalview.datamodel.Annotation[] (after)} - */ - private Object[] parseRangeAnnotation(org.vamsas.objects.core.RangeAnnotation annotation) { - // set these attributes by looking in the annotation to decide what kind of alignment annotation rows will be made - // TODO: potentially we might make several annotation rows from one vamsas alignment annotation. the jv2Vobj binding mechanism - // may not quite cope with this (without binding an array of annotations to a vamsas alignment annotation) - // summary flags saying what we found over the set of annotation rows. - boolean[] AeContent = new boolean[] { false, false, false, false, false}; - int[] rangeMap = getMapping(annotation); - jalview.datamodel.Annotation[][] anot=new jalview.datamodel.Annotation[][] { - new jalview.datamodel.Annotation[rangeMap.length], - new jalview.datamodel.Annotation[rangeMap.length] - }; - boolean mergeable=true; //false if 'after positions cant be placed on same annotation row as positions. - - if (annotation.getAnnotationElementCount()>0) { - AnnotationElement ae[] = annotation.getAnnotationElement(); - for (int aa = 0; aa < ae.length; aa++) - { - int pos = ae[aa].getPosition()-1;// pos counts from 1 to (|seg.start-seg.end|+1) - if (pos>=0 && pos0) { - // have imported valid description string - AeContent[HASDESCSTR]=true; - } - } - String dc = null;//ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter(); - String ss = null;//ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure(); - java.awt.Color colour = null; - if (ae[aa].getGlyphCount()>0) { - Glyph[] glyphs = ae[aa].getGlyph(); - for (int g=0; g0) { - AeContent[HASVALS]=true; - if (ae[aa].getValueCount()>1) { - Cache.log.warn("ignoring additional "+(ae[aa].getValueCount()-1)+"values in annotation element."); - } - val = ae[aa].getValue(0); - } - if (colour==null) { - anot[row][pos]=new jalview.datamodel.Annotation((dc!=null) ? dc : "", desc, (ss!=null)?ss.charAt(0):' ', val); - } else { - anot[row][pos]=new jalview.datamodel.Annotation((dc!=null) ? dc : "", desc, (ss!=null)?ss.charAt(0):' ', val, colour); - } - } else { - Cache.log.warn("Ignoring out of bound annotation element "+aa+" in "+annotation.getVorbaId().getId()); - } - } - // decide on how many annotation rows are needed. - if (mergeable) { - for (int i=0; i1) { - // do some interpolation *between* points - if (arow[lastval]!=null) { - float interval = arow[i].value-arow[lastval].value; - interval/=i-lastval; - float base = arow[lastval].value; - for (int ip=lastval+1,np=0; ipmax) { max=arow[i].value; } - } - // make tooltip and display char value - if (!has[HASDESCSTR]) arow[i].description = arow[i].value + ""; - if (!has[HASDC]) arow[i].displayCharacter=arow[i].value+""; - } - } - int type=jalview.datamodel.AlignmentAnnotation.LINE_GRAPH; - if (has[HASHPHOB]) { - type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; - } - jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow, min, max, type); - } else { - jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow); - jan.setThreshold(null); - } - if (annotation.getLinkCount()>0) { - Cache.log.warn("Ignoring "+annotation.getLinkCount()+"links added to AlignmentAnnotation."); - } - if (annotation.getModifiable()) { - jan.editable=true; - } - - if (annotation.getPropertyCount()>0) { - // look for special jalview properties - org.vamsas.objects.core.Property[] props=annotation.getProperty(); - for (int p=0;p0) - jan.graphGroup = Integer.parseInt(annotation.getGroup()); - } catch (Exception e) { - Cache.log.info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly."); - } - } - } - } - - return jan; - - } - - return null; - } - - private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta) { - int[] se = getBounds(dseta); - SequenceFeature sf = new jalview.datamodel.SequenceFeature(dseta.getType(), - dseta.getDescription(), dseta.getStatus(), se[0], se[1], dseta - .getGroup()); - if (dseta.getLinkCount() > 0) - { - Link[] links = dseta.getLink(); - for (int i = 0; i < links.length; i++) - { - sf.addLink(links[i].getContent() + "|" + links[i].getHref()); - } - } - return sf; - } - - /** - * get real bounds of a RangeType's specification. start and end are an - * inclusive range within which all segments and positions lie. - * TODO: refactor to vamsas utils - * @param dseta - * @return int[] { start, end} - */ - private int[] getBounds(RangeType dseta) { - if (dseta != null) - { - int[] se = null; - if (dseta.getSegCount()>0 && dseta.getPosCount()>0) - throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); - if (dseta.getSegCount() > 0) - { - se = getSegRange(dseta.getSeg(0),true); - for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++) - { - int nse[] = getSegRange(dseta.getSeg(s), true); - if (se[0] > nse[0]) - se[0] = nse[0]; - if (se[1] < nse[1]) - se[1] = nse[1]; - } - } - if (dseta.getPosCount() > 0) - { - // could do a polarity for pos range too. and pass back indication of discontinuities. - int pos = dseta.getPos(0).getI(); - se = new int[] { pos, pos }; - for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) - { - pos = dseta.getPos(p).getI(); - if (se[0] > pos) - se[0] = pos; - if (se[1] < pos) - se[1] = pos; - } - } - return se; - } - return null; - } - /** - * map from a rangeType's internal frame to the referenced object's coordinate frame. - * @param dseta - * @return int [] { ref(pos)...} for all pos in rangeType's frame. - */ - private int[] getMapping(RangeType dseta) { - Vector posList=new Vector(); - if (dseta != null) - { - int[] se = null; - if (dseta.getSegCount()>0 && dseta.getPosCount()>0) - throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); - if (dseta.getSegCount() > 0) - { - for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++) - { - se = getSegRange(dseta.getSeg(s), false); - int se_end=se[1-se[2]]+(se[2]==0 ? 1 : -1); - for (int p=se[se[2]]; p!=se_end; p+=se[2]==0 ? 1 : -1 ) { - posList.add(new Integer(p)); - } - } - } - else if (dseta.getPosCount() > 0) - { - int pos = dseta.getPos(0).getI(); - - for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) - { - pos = dseta.getPos(p).getI(); - posList.add(new Integer(pos)); - } - } - } - if (posList!=null && posList.size()>0) { - int[] range=new int[posList.size()]; - for (int i=0; i 0) + { + an.setGraph(true); // aa[i].graph); + } + else + { + an.setGraph(false); + } + an.setLabel(aa[i].label); + an.setProvenance(dummyProvenance()); // get provenance as user + // created, or jnet, or + // something else. + an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote - + // originally we + // were going to + // store + // graphGroup in + // the Jalview + // specific + // bits. + AnnotationElement ae; + for (int a = 0; a < aa[i].annotations.length; a++) + { + if (aa[i].annotations[a] == null) + { + continue; + } + + ae = new AnnotationElement(); + ae.setDescription(aa[i].annotations[a].description); + ae.addGlyph(new Glyph()); + ae.getGlyph(0) + .setContent(aa[i].annotations[a].displayCharacter); // assume + // jax-b + // takes + // care + // of + // utf8 + // translation + if (aa[i].graph != + jalview.datamodel.AlignmentAnnotation.NO_GRAPH) + { + ae.addValue(aa[i].annotations[a].value); + } + ae.setPosition(gapMap[a] + 1); // position w.r.t. AlignmentSequence + // symbols + if (aa[i].annotations[a].secondaryStructure != ' ') + { + // we only write an annotation where it really exists. + Glyph ss = new Glyph(); + ss + .setDict(org.vamsas.objects.utils.GlyphDictionary. + PROTEIN_SS_3STATE); + ss.setContent(String + .valueOf(aa[i].annotations[a]. + secondaryStructure)); + ae.addGlyph(ss); + } + an.addAnnotationElement(ae); + } + } + else + { + // update reference sequence Annotation + if (an.getModifiable()) + { + // verify existing alignment sequence annotation is up to date + System.out.println("update alignment sequence annotation."); + } + else + { + // verify existing alignment sequence annotation is up to date + System.out + .println( + "make new alignment sequence annotation if modification has happened."); + } + } + } + else + { + // add Alignment Annotation + org.vamsas.objects.core.AlignmentAnnotation an = (org.vamsas. + objects.core.AlignmentAnnotation) getjv2vObj(aa[i]); + if (an == null) + { + an = new org.vamsas.objects.core.AlignmentAnnotation(); + an.setType("jalview:AnnotationRow"); + an.setDescription(aa[i].description); + alignment.addAlignmentAnnotation(an); + Seg vSeg = new Seg(); + vSeg.setStart(1); + vSeg.setInclusive(true); + vSeg.setEnd(jal.getWidth()); + an.addSeg(vSeg); + if (aa[i].graph > 0) + { + an.setGraph(true); // aa[i].graph); + } + an.setLabel(aa[i].label); + an.setProvenance(dummyProvenance()); + if (aa[i].graph != aa[i].NO_GRAPH) + { + an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote - + // originally we + // were going to + // store + // graphGroup in + // the Jalview + // specific + // bits. + an.setGraph(true); + } + else + { + an.setGraph(false); + } + AnnotationElement ae; + + for (int a = 0; a < aa[i].annotations.length; a++) + { + if ( (aa[i] == null) || (aa[i].annotations[a] == null)) + { + continue; + } + + ae = new AnnotationElement(); + ae.setDescription(aa[i].annotations[a].description); + ae.addGlyph(new Glyph()); + ae.getGlyph(0) + .setContent(aa[i].annotations[a].displayCharacter); // assume + // jax-b + // takes + // care + // of + // utf8 + // translation + ae.addValue(aa[i].annotations[a].value); + ae.setPosition(a + 1); + if (aa[i].annotations[a].secondaryStructure != ' ') + { + Glyph ss = new Glyph(); + ss + .setDict(org.vamsas.objects.utils.GlyphDictionary. + PROTEIN_SS_3STATE); + ss.setContent(String + .valueOf(aa[i].annotations[a]. + secondaryStructure)); + ae.addGlyph(ss); + } + an.addAnnotationElement(ae); + } + if (aa[i].editable) + { + //an.addProperty(newProperty("jalview:editable", null, "true")); + an.setModifiable(true); + } + if (aa[i].graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH) + { + an.setGraph(true); + an.setGroup(Integer.toString(aa[i].graphGroup)); + an.addProperty(newProperty("jalview:graphType", null, + ( (aa[i].graph == + jalview.datamodel.AlignmentAnnotation. + BAR_GRAPH) ? "BAR_GRAPH" : + "LINE_GRAPH"))); + + /** and on and on.. + vProperty=new Property(); + vProperty.setName("jalview:graphThreshhold"); + vProperty.setContent(aa[i].threshold); + */ + + } + } + else + { + if (an.getModifiable()) + { + // verify annotation - update (perhaps) + Cache.log.info( + "update alignment sequence annotation. not yet implemented."); + } + else + { + // verify annotation - update (perhaps) + Cache.log.info("updated alignment sequence annotation added."); + } + } + } + } + } + // ///////////////////////////////////////////////////// + + // ////////////////////////////////////////////// + // /SAVE THE TREES + // ///////////////////////////////// + // FIND ANY ASSOCIATED TREES + if (Desktop.desktop != null) + { + javax.swing.JInternalFrame[] frames = Desktop.instance.getAllFrames(); + + for (int t = 0; t < frames.length; t++) + { + if (frames[t] instanceof TreePanel) + { + TreePanel tp = (TreePanel) frames[t]; + + if (tp.getAlignment() == jal) + { + Tree tree = (Tree) getjv2vObj(tp); + if (tree == null) + { + tree = new Tree(); + bindjvvobj(tp, tree); + tree.setTitle(tp.getTitle()); + Newick newick = new Newick(); + // TODO: translate sequenceI to leaf mappings to vamsas + // references - see tree specification in schema. + newick.setContent(tp.getTree().toString()); + newick.setTitle(tp.getTitle()); + tree.addNewick(newick); + tree.setProvenance(makeTreeProvenance(jal, tp)); + alignment.addTree(tree); + } + else + { + if (tree.getModifiable()) + { + // verify any changes. + System.out.println("Update tree in document."); + } + else + { + System.out + .println("Add modified tree as new tree in document."); + } + } + } + } + } + } + // Store Jalview specific stuff in the Jalview appData + // not implemented in the SimpleDoc interface. + } + + catch (Exception ex) + { + ex.printStackTrace(); + } + + } + + private Property newProperty(String name, String type, String content) + { + Property vProperty = new Property(); + vProperty.setName(name); + if (type != null) + { + vProperty.setType(type); + } + else + { + vProperty.setType("String"); + } + vProperty.setContent(content); + return vProperty; + } + + /** + * correctly create a RangeAnnotation from a jalview sequence feature + * + * @param dsa + * (typically DataSetAnnotations or AlignmentSequenceAnnotation) + * @param feature + * (the feature to be mapped from) + * @return + */ + private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa, + SequenceFeature feature) + { + dsa.setType(feature.getType()); + Seg vSeg = new Seg(); + vSeg.setStart(feature.getBegin()); + vSeg.setEnd(feature.getEnd()); + vSeg.setInclusive(true); + dsa.addSeg(vSeg); + dsa.setDescription(feature.getDescription()); + dsa.setStatus(feature.getStatus()); + if (feature.links != null && feature.links.size() > 0) + { + for (int i = 0, iSize = feature.links.size(); i < iSize; i++) + { + String link = (String) feature.links.elementAt(i); + int sep = link.indexOf('|'); + if (sep > -1) + { + Link vLink = new Link(); + if (sep > 0) + { + vLink.setContent(link.substring(0, sep - 1)); + } + else + { + vLink.setContent(""); + } + vLink.setHref(link.substring(sep + 1)); // TODO: validate href. + dsa.addLink(vLink); + } + } + } + dsa.setGroup(feature.getFeatureGroup()); + return dsa; + } + + /** + * correctly creates provenance for trees calculated on an alignment by + * jalview. + * + * @param jal + * @param tp + * @return + */ + private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp) + { + Provenance prov = new Provenance(); + prov.addEntry(new Entry()); + prov.getEntry(0).setAction("imported " + tp.getTitle()); + prov.getEntry(0).setUser(provEntry.getUser()); + prov.getEntry(0).setApp(provEntry.getApp()); + prov.getEntry(0).setDate(provEntry.getDate()); + if (tp.getTree().hasOriginalSequenceData()) + { + Input vInput = new Input(); + // LATER: check to see if tree input data is contained in this alignment - + // or just correctly resolve the tree's seqData to the correct alignment in + // the document. + // vInput.setObjRef(getjv2vObj(jal)); + vInput.setObjRef(getjv2vObj(tp.getViewPort())); + prov.getEntry(0).setAction("created " + tp.getTitle()); + prov.getEntry(0).addInput(vInput); + vInput.setName("jalview:seqdist"); + prov.getEntry(0).addParam(new Param()); + prov.getEntry(0).getParam(0).setName("treeType"); + prov.getEntry(0).getParam(0).setType("utf8"); + prov.getEntry(0).getParam(0).setContent("NJ"); + + int ranges[] = tp.getTree().seqData.getVisibleContigs(); + // VisibleContigs are with respect to alignment coordinates. Still need offsets + int start = tp.getTree().seqData.getAlignmentOrigin(); + for (int r = 0; r < ranges.length; r += 2) + { + Seg visSeg = new Seg(); + visSeg.setStart(1 + start + ranges[r]); + visSeg.setEnd(start + ranges[r + 1]); + visSeg.setInclusive(true); + vInput.addSeg(visSeg); + } + } + return prov; + } + + /** + * + * @param tp + * @return Object[] { AlignmentView, AlignmentI - reference alignment for + * input } + */ + private Object[] recoverInputData(Provenance tp) + { + for (int pe = 0; pe < tp.getEntryCount(); pe++) + { + if (tp.getEntry(pe).getInputCount() > 0) + { + if (tp.getEntry(pe).getInputCount() > 1) + { + Cache.log.warn("Ignoring additional input spec in provenance entry " + + tp.getEntry(pe).toString()); + } + // LATER: deal sensibly with multiple inputs. + Input vInput = tp.getEntry(pe).getInput(0); + if (vInput.getObjRef() instanceof org.vamsas.objects.core.Alignment) + { + // recover an AlignmentView for the input data + AlignViewport javport = (AlignViewport) getvObj2jv( (org.vamsas. + client.Vobject) vInput + .getObjRef()); + jalview.datamodel.AlignmentI jal = javport.getAlignment(); + jalview.datamodel.CigarArray view = javport.getAlignment(). + getCompactAlignment(); + int from = 1, to = jal.getWidth(); + int offset = 0; // deleteRange modifies its frame of reference + for (int r = 0, s = vInput.getSegCount(); r < s; r++) + { + Seg visSeg = vInput.getSeg(r); + int se[] = getSegRange(visSeg, true); // jalview doesn't do bidirection alignments yet. + if (to < se[1]) + { + Cache.log.warn("Ignoring invalid segment in InputData spec."); + } + else + { + if (se[0] > from) + { + view.deleteRange(offset + from - 1, offset + se[0] - 2); + offset -= se[0] - from; + } + from = se[1] + 1; + } + } + if (from < to) + { + view.deleteRange(offset + from - 1, offset + to - 1); // final deletion - TODO: check off by + // one for to + } + return new Object[] + { + new AlignmentView(view), jal}; + } + } + } + Cache.log.debug("Returning null for input data recovery from provenance."); + return null; + } + + /** + * get start 0) + { + DbRef[] dbref = vdseq.getDbRef(); + for (int db = 0; db < dbref.length; db++) + { + jalview.datamodel.DBRefEntry dbr = (jalview.datamodel.DBRefEntry) + getvObj2jv(dbref[db]); + if (dbr == null) + { + // add new dbref + dsseq.addDBRef(dbr = new jalview.datamodel.DBRefEntry + ( + dbref[db].getSource().toString(), + dbref[db].getVersion().toString(), + dbref[db].getAccessionId().toString())); + bindjvvobj(dbr, dbref[db]); + } + } + } + } + + if (newds) + { + SequenceI[] seqs = new SequenceI[dsseqs.size()]; + for (i = 0, iSize = dsseqs.size(); i < iSize; i++) + { + seqs[i] = (SequenceI) dsseqs.elementAt(i); + dsseqs.setElementAt(null, i); + } + jdataset = new jalview.datamodel.Alignment(seqs); + Cache.log.debug("New vamsas dataset imported into jalview."); + bindjvvobj(jdataset, dataset); + } + // //////// + // add any new dataset sequence feature annotations + if (dataset.getDataSetAnnotations() != null) + { + for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++) + { + DataSetAnnotations dseta = dataset.getDataSetAnnotations(dsa); + SequenceI dsSeq = (SequenceI) getvObj2jv( (Vobject) dseta.getSeqRef()); + if (dsSeq == null) + { + jalview.bin.Cache.log.warn( + "Couldn't resolve jalview sequenceI for dataset object reference " + + ( (Vobject) dataset.getDataSetAnnotations(dsa).getSeqRef()). + getVorbaId().getId()); + } + else + { + if (dseta.getAnnotationElementCount() == 0) + { + jalview.datamodel.SequenceFeature sf = (jalview.datamodel. + SequenceFeature) getvObj2jv(dseta); + if (sf == null) + { + dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dseta)); + bindjvvobj(sf, dseta); + } + } + else + { + // TODO: deal with alignmentAnnotation style annotation + // appearing on dataset sequences. + // JBPNote: we could just add them to all alignments but + // that may complicate cross references in the jalview + // datamodel + Cache.log.warn("Ignoring dataset annotation with annotationElements. Not yet supported in jalview."); + } + } + } + } + + if (dataset.getAlignmentCount() > 0) + { + // LOAD ALIGNMENTS from DATASET + + for (int al = 0, nal = dataset.getAlignmentCount(); al < nal; al++) + { + org.vamsas.objects.core.Alignment alignment = dataset.getAlignment( + al); + AlignViewport av = (AlignViewport) getvObj2jv(alignment); + jalview.datamodel.AlignmentI jal = null; + if (av != null) + { + jal = av.getAlignment(); + } + iSize = alignment.getAlignmentSequenceCount(); + boolean newal = (jal == null) ? true : false; + Vector newasAnnots = new Vector(); + char gapChar = ' '; // default for new alignments read in from the document + if (jal != null) + { + dsseqs = jal.getSequences(); // for merge/update + gapChar = jal.getGapCharacter(); + } + else + { + dsseqs = new Vector(); + } + char valGapchar = alignment.getGapChar().charAt(0); + for (i = 0; i < iSize; i++) + { + AlignmentSequence valseq = alignment.getAlignmentSequence(i); + jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq); + if (alseq != null) + { + //TODO: upperCase/LowerCase situation here ? do we allow it ? + //if (!alseq.getSequence().equals(valseq.getSequence())) { + // throw new Error("Broken! - mismatch of dataset sequence and jalview internal dataset sequence."); + if (Cache.log.isDebugEnabled()) + { + Cache.log.debug("Updating apparently edited sequence " + + alseq.getName()); + } + // this might go *horribly* wrong + alseq.setSequence(new String(valseq.getSequence()).replace( + valGapchar, gapChar)); + jremain--; + } + else + { + alseq = new jalview.datamodel.Sequence( + valseq.getName(), + valseq.getSequence().replace(valGapchar, gapChar), + valseq.getStart(), + valseq.getEnd()); + + Vobject datsetseq = (Vobject) valseq.getRefid(); + if (datsetseq != null) + { + alseq.setDatasetSequence( (SequenceI) getvObj2jv(datsetseq)); // exceptions if AlignemntSequence reference isn't a simple SequenceI + } + else + { + Cache.log.error( + "Invalid dataset sequence id (null) for alignment sequence " + + valseq.getVorbaId()); + } + bindjvvobj(alseq, valseq); + alseq.setVamsasId(valseq.getVorbaId().getId()); + dsseqs.add(alseq); + } + if (valseq.getAlignmentSequenceAnnotationCount() > 0) + { + AlignmentSequenceAnnotation[] vasannot = valseq. + getAlignmentSequenceAnnotation(); + for (int a = 0; a < vasannot.length; a++) + { + jalview.datamodel.AlignmentAnnotation asa = (jalview. + datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO: 1:many jalview alignment sequence annotations + if (asa == null) + { + int se[] = getBounds(vasannot[a]); + asa = getjAlignmentAnnotation(jal, vasannot[a]); + asa.sequenceRef = alseq; + asa.createSequenceMapping(alseq, alseq.getStart() + se[0], false); // TODO: verify that positions in alseqAnnotation correspond to ungapped residue positions. + bindjvvobj(asa, vasannot[a]); + newasAnnots.add(asa); + } + else + { + // update existing annotation - can do this in place + if (vasannot[a].getModifiable()) + { + Cache.log.info( + "UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation"); + // TODO: should at least replace with new one - otherwise things will break + // basically do this: + // int se[] = getBounds(vasannot[a]); + // asa.update(getjAlignmentAnnotation(jal, vasannot[a])); // update from another annotation object in place. + // asa.createSequenceMapping(alseq, se[0], false); + + } + } + } + } + } + if (jal == null) + { + SequenceI[] seqs = new SequenceI[dsseqs.size()]; + for (i = 0, iSize = dsseqs.size(); i < iSize; i++) + { + seqs[i] = (SequenceI) dsseqs.elementAt(i); + dsseqs.setElementAt(null, i); + } + jal = new jalview.datamodel.Alignment(seqs); + Cache.log.debug("New vamsas alignment imported into jalview " + + alignment.getVorbaId().getId()); + jal.setDataset(jdataset); + } + if (newasAnnots != null && newasAnnots.size() > 0) + { + // Add the new sequence annotations in to the alignment. + for (int an = 0, anSize = newasAnnots.size(); an < anSize; an++) + { + jal.addAnnotation( (AlignmentAnnotation) newasAnnots.elementAt( + an)); + // TODO: check if anything has to be done - like calling adjustForAlignment or something. + newasAnnots.setElementAt(null, an); + } + newasAnnots = null; + } + // ////////////////////////////////////////// + // //LOAD ANNOTATIONS FOR THE ALIGNMENT + // //////////////////////////////////// + if (alignment.getAlignmentAnnotationCount() > 0) + { + org.vamsas.objects.core.AlignmentAnnotation[] an = alignment. + getAlignmentAnnotation(); + + for (int j = 0; j < an.length; j++) + { + jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel. + AlignmentAnnotation) getvObj2jv(an[j]); + if (jan != null) + { + // update or stay the same. + // TODO: should at least replace with a new one - otherwise things will break + // basically do this: + // jan.update(getjAlignmentAnnotation(jal, an[a])); // update from another annotation object in place. + + Cache.log.debug("update from vamsas alignment annotation to existing jalview alignment annotation."); + if (an[j].getModifiable()) + { + // TODO: user defined annotation is totally mutable... - so load it up or throw away if locally edited. + Cache.log.info( + "NOT IMPLEMENTED - Recovering user-modifiable annotation - yet..."); + } + // TODO: compare annotation element rows + // TODO: compare props. + } + else + { + jan = getjAlignmentAnnotation(jal, an[j]); + jal.addAnnotation(jan); + bindjvvobj(jan, an[j]); + } + } + } + AlignFrame alignFrame; + if (av == null) + { + Cache.log.debug("New alignframe for alignment " + + alignment.getVorbaId()); + // /////////////////////////////// + // construct alignment view + alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + av = alignFrame.getViewport(); + String title = alignment.getProvenance().getEntry(alignment. + getProvenance().getEntryCount() - 1).getAction(); + if (alignment.getPropertyCount() > 0) + { + for (int p = 0, pe = alignment.getPropertyCount(); p < pe; p++) + { + if (alignment.getProperty(p).getName().equals( + "jalview:AlTitle")) + { + title = alignment.getProperty(p).getContent(); + } + } + } + // TODO: automatically create meaningful title for a vamsas alignment using its provenance. + jalview.gui.Desktop.addInternalFrame(alignFrame, + title + "(" + alignment.getVorbaId() + ")", + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + bindjvvobj(av, alignment); + } + else + { + // find the alignFrame for jal. + // TODO: fix this so we retrieve the alignFrame handing av *directly* + alignFrame = getAlignFrameFor(av); + } + // LOAD TREES + // ///////////////////////////////////// + if (alignment.getTreeCount() > 0) + { + + for (int t = 0; t < alignment.getTreeCount(); t++) + { + Tree tree = alignment.getTree(t); + TreePanel tp = (TreePanel) getvObj2jv(tree); + if (tp != null) + { + Cache.log.info( + "Update from vamsas document to alignment associated tree not implemented yet."); + } + else + { + // make a new tree + Object[] idata = this.recoverInputData(tree.getProvenance()); + try + { + AlignmentView inputData = null; + if (idata != null && idata[0] != null) + { + inputData = (AlignmentView) idata[0]; + } + tp = alignFrame.ShowNewickTree( + new jalview.io.NewickFile(tree.getNewick(0).getContent()), + tree.getNewick(0).getTitle() + " (" + tree.getVorbaId() + + ")", inputData, + 600, 500, + t * 20 + 50, t * 20 + 50); + bindjvvobj(tp, tree); + } + catch (Exception e) + { + Cache.log.warn("Problems parsing treefile '" + + tree.getNewick(0).getContent() + "'", e); + } + } + } + } + + } + } + } + } + } + + // bitfields - should be a template in j1.5 + private static int HASSECSTR = 0; + private static int HASVALS = 1; + private static int HASHPHOB = 2; + private static int HASDC = 3; + private static int HASDESCSTR = 4; + private static int HASTWOSTATE = 5; // not used yet. + /** + * parses the AnnotationElements - if they exist - into jalview.datamodel.Annotation[] rows + * Two annotation rows are made if there are distinct annotation for both at 'pos' and 'after pos' at any particular site. + * @param annotation + * @return { boolean[static int constants ], int[ae.length] - map to annotated object frame, jalview.datamodel.Annotation[], jalview.datamodel.Annotation[] (after)} + */ + private Object[] parseRangeAnnotation(org.vamsas.objects.core.RangeAnnotation + annotation) + { + // set these attributes by looking in the annotation to decide what kind of alignment annotation rows will be made + // TODO: potentially we might make several annotation rows from one vamsas alignment annotation. the jv2Vobj binding mechanism + // may not quite cope with this (without binding an array of annotations to a vamsas alignment annotation) + // summary flags saying what we found over the set of annotation rows. + boolean[] AeContent = new boolean[] + { + false, false, false, false, false}; + int[] rangeMap = getMapping(annotation); + jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][] + { + new jalview.datamodel.Annotation[rangeMap.length], + new jalview.datamodel.Annotation[rangeMap.length] + }; + boolean mergeable = true; //false if 'after positions cant be placed on same annotation row as positions. + + if (annotation.getAnnotationElementCount() > 0) + { + AnnotationElement ae[] = annotation.getAnnotationElement(); + for (int aa = 0; aa < ae.length; aa++) + { + int pos = ae[aa].getPosition() - 1; // pos counts from 1 to (|seg.start-seg.end|+1) + if (pos >= 0 && pos < rangeMap.length) + { + int row = ae[aa].getAfter() ? 1 : 0; + if (anot[row][pos] != null) + { + // only time this should happen is if the After flag is set. + Cache.log.debug("Ignoring duplicate annotation site at " + pos); + continue; + } + if (anot[1 - row][pos] != null) + { + mergeable = false; + } + String desc = ""; + if (ae[aa].getDescription() != null) + { + desc = ae[aa].getDescription(); + if (desc.length() > 0) + { + // have imported valid description string + AeContent[HASDESCSTR] = true; + } + } + String dc = null; //ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter(); + String ss = null; //ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure(); + java.awt.Color colour = null; + if (ae[aa].getGlyphCount() > 0) + { + Glyph[] glyphs = ae[aa].getGlyph(); + for (int g = 0; g < glyphs.length; g++) + { + if (glyphs[g].getDict().equals(org.vamsas.objects.utils. + GlyphDictionary.PROTEIN_SS_3STATE)) + { + ss = glyphs[g].getContent(); + AeContent[HASSECSTR] = true; + } + else if (glyphs[g].getDict().equals(org.vamsas.objects.utils. + GlyphDictionary. + PROTEIN_HD_HYDRO)) + { + Cache.log.debug("ignoring hydrophobicity glyph marker."); + AeContent[HASHPHOB] = true; + char c = (dc = glyphs[g].getContent()).charAt(0); + // dc may get overwritten - but we still set the colour. + colour = new java.awt.Color(c == '+' ? 255 : 0, + c == '.' ? 255 : 0, + c == '-' ? 255 : 0); + + } + else if (glyphs[g].getDict().equals(org.vamsas.objects.utils. + GlyphDictionary.DEFAULT)) + { + dc = glyphs[g].getContent(); + AeContent[HASDC] = true; + } + else + { + Cache.log.debug("Ignoring unknown glyph type " + + glyphs[g].getDict()); + } + } + } + float val = 0; + if (ae[aa].getValueCount() > 0) + { + AeContent[HASVALS] = true; + if (ae[aa].getValueCount() > 1) + { + Cache.log.warn("ignoring additional " + + (ae[aa].getValueCount() - 1) + + "values in annotation element."); + } + val = ae[aa].getValue(0); + } + if (colour == null) + { + anot[row][pos] = new jalview.datamodel.Annotation( (dc != null) ? + dc : "", desc, (ss != null) ? ss.charAt(0) : ' ', val); + } + else + { + anot[row][pos] = new jalview.datamodel.Annotation( (dc != null) ? + dc : "", desc, (ss != null) ? ss.charAt(0) : ' ', val, colour); + } + } + else + { + Cache.log.warn("Ignoring out of bound annotation element " + aa + + " in " + annotation.getVorbaId().getId()); + } + } + // decide on how many annotation rows are needed. + if (mergeable) + { + for (int i = 0; i < anot[0].length; i++) + { + if (anot[1][i] != null) + { + anot[0][i] = anot[1][i]; + anot[0][i].description = anot[0][i].description + " (after)"; + AeContent[HASDESCSTR] = true; // we have valid description string data + anot[1][i] = null; + } + } + anot[1] = null; + } + else + { + for (int i = 0; i < anot[0].length; i++) + { + anot[1][i].description = anot[1][i].description + " (after)"; + } + } + return new Object[] + { + AeContent, rangeMap, anot[0], anot[1]}; + } + else + { + // no annotations to parse. Just return an empty annotationElement[] array. + return new Object[] + { + AeContent, rangeMap, anot[0], anot[1]}; + } + // return null; + } + + /** + * @param jal the jalview alignment to which the annotation will be attached (ideally - freshly updated from corresponding vamsas alignment) + * @param annotation + * @return unbound jalview alignment annotation object. + */ + private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(jalview. + datamodel.AlignmentI jal, + org.vamsas.objects.core.RangeAnnotation annotation) + { + jalview.datamodel.AlignmentAnnotation jan = null; + if (annotation == null) + { + return null; + } + // boolean hasSequenceRef=annotation.getClass().equals(org.vamsas.objects.core.AlignmentSequenceAnnotation.class); + //boolean hasProvenance=hasSequenceRef || (annotation.getClass().equals(org.vamsas.objects.core.AlignmentAnnotation.class)); + /*int se[] = getBounds(annotation); + if (se==null) + se=new int[] {0,jal.getWidth()-1}; + */ + Object[] parsedRangeAnnotation = parseRangeAnnotation(annotation); + String a_label = annotation.getLabel(); + String a_descr = annotation.getDescription(); + if (a_label == null || a_label.length() == 0) + { + a_label = annotation.getType(); + if (a_label.length() == 0) + { + a_label = "Unamed annotation"; + } + } + if (a_descr == null || a_descr.length() == 0) + { + a_descr = "Annotation of type '" + annotation.getType() + "'"; + } + if (parsedRangeAnnotation == null) + { + Cache.log.debug( + "Inserting empty annotation row elements for a whole-alignment annotation."); + + } + else + { + if (parsedRangeAnnotation[3] != null) + { + Cache.log.warn("Ignoring 'After' annotation row in " + + annotation.getVorbaId()); + } + jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) + parsedRangeAnnotation[2]; + boolean[] has = (boolean[]) parsedRangeAnnotation[0]; + // VAMSAS: getGraph is only on derived annotation for alignments - in this way its 'odd' - there is already an existing TODO about removing this flag as being redundant + /*if ((annotation.getClass().equals(org.vamsas.objects.core.AlignmentAnnotation.class) && ((org.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph()) + || (hasSequenceRef=true && ((org.vamsas.objects.core.AlignmentSequenceAnnotation)annotation).getGraph())) { + */ + if (has[HASVALS]) + { + // make bounds and automatic description strings for jalview user's benefit (these shouldn't be written back to vamsas document) + boolean first = true; + float min = 0, max = 1; + int lastval = 0; + for (int i = 0; i < arow.length; i++) + { + if (arow[i] != null) + { + if (i - lastval > 1) + { + // do some interpolation *between* points + if (arow[lastval] != null) + { + float interval = arow[i].value - arow[lastval].value; + interval /= i - lastval; + float base = arow[lastval].value; + for (int ip = lastval + 1, np = 0; ip < i; np++, ip++) + { + arow[ip] = new jalview.datamodel.Annotation("", "", ' ', + interval * np + base); + // NB - Interpolated points don't get a tooltip and description. + } + } + } + lastval = i; + // check range - shouldn't we have a min and max property in the annotation object ? + if (first) + { + min = max = arow[i].value; + first = false; + } + else + { + if (arow[i].value < min) + { + min = arow[i].value; + } + else if (arow[i].value > max) + { + max = arow[i].value; + } + } + // make tooltip and display char value + if (!has[HASDESCSTR]) + { + arow[i].description = arow[i].value + ""; + } + if (!has[HASDC]) + { + arow[i].displayCharacter = arow[i].value + ""; + } + } + } + int type = jalview.datamodel.AlignmentAnnotation.LINE_GRAPH; + if (has[HASHPHOB]) + { + type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; + } + jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow, + min, max, type); + } + else + { + jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow); + jan.setThreshold(null); + } + if (annotation.getLinkCount() > 0) + { + Cache.log.warn("Ignoring " + annotation.getLinkCount() + + "links added to AlignmentAnnotation."); + } + if (annotation.getModifiable()) + { + jan.editable = true; + } + + if (annotation.getPropertyCount() > 0) + { + // look for special jalview properties + org.vamsas.objects.core.Property[] props = annotation.getProperty(); + for (int p = 0; p < props.length; p++) + { + if (props[p].getName().equalsIgnoreCase("jalview:graphType")) + { + try + { + // probably a jalview annotation graph so recover the visualization hints. + jan.graph = jalview.datamodel.AlignmentAnnotation. + getGraphValueFromString(props[p].getContent()); + } + catch (Exception e) + { + Cache.log.debug( + "Invalid graph type value in jalview:graphType property."); + } + try + { + if (annotation.getGroup() != null && + annotation.getGroup().length() > 0) + { + jan.graphGroup = Integer.parseInt(annotation.getGroup()); + } + } + catch (Exception e) + { + Cache.log.info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly."); + } + } + } + } + + return jan; + + } + + return null; + } + + private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta) + { + int[] se = getBounds(dseta); + SequenceFeature sf = new jalview.datamodel.SequenceFeature(dseta.getType(), + dseta.getDescription(), dseta.getStatus(), se[0], se[1], dseta + .getGroup()); + if (dseta.getLinkCount() > 0) + { + Link[] links = dseta.getLink(); + for (int i = 0; i < links.length; i++) + { + sf.addLink(links[i].getContent() + "|" + links[i].getHref()); + } + } + return sf; + } + + /** + * get real bounds of a RangeType's specification. start and end are an + * inclusive range within which all segments and positions lie. + * TODO: refactor to vamsas utils + * @param dseta + * @return int[] { start, end} + */ + private int[] getBounds(RangeType dseta) + { + if (dseta != null) + { + int[] se = null; + if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) + { + throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); + } + if (dseta.getSegCount() > 0) + { + se = getSegRange(dseta.getSeg(0), true); + for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++) + { + int nse[] = getSegRange(dseta.getSeg(s), true); + if (se[0] > nse[0]) + { + se[0] = nse[0]; + } + if (se[1] < nse[1]) + { + se[1] = nse[1]; + } + } + } + if (dseta.getPosCount() > 0) + { + // could do a polarity for pos range too. and pass back indication of discontinuities. + int pos = dseta.getPos(0).getI(); + se = new int[] + { + pos, pos}; + for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) + { + pos = dseta.getPos(p).getI(); + if (se[0] > pos) + { + se[0] = pos; + } + if (se[1] < pos) + { + se[1] = pos; + } + } + } + return se; + } + return null; + } + + /** + * map from a rangeType's internal frame to the referenced object's coordinate frame. + * @param dseta + * @return int [] { ref(pos)...} for all pos in rangeType's frame. + */ + private int[] getMapping(RangeType dseta) + { + Vector posList = new Vector(); + if (dseta != null) + { + int[] se = null; + if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) + { + throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); + } + if (dseta.getSegCount() > 0) + { + for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++) + { + se = getSegRange(dseta.getSeg(s), false); + int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1); + for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1) + { + posList.add(new Integer(p)); + } + } + } + else if (dseta.getPosCount() > 0) + { + int pos = dseta.getPos(0).getI(); + + for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) + { + pos = dseta.getPos(p).getI(); + posList.add(new Integer(pos)); + } + } + } + if (posList != null && posList.size() > 0) + { + int[] range = new int[posList.size()]; + for (int i = 0; i < range.length; i++) + { + range[i] = ( (Integer) posList.elementAt(i)).intValue(); + } + posList.clear(); + return range; + } + return null; + } + + /* not needed now. + * Provenance getVamsasProvenance(jalview.datamodel.Provenance jprov) { + jalview.datamodel.ProvenanceEntry[] entries = null; + // TODO: fix App and Action here. + Provenance prov = new Provenance(); + org.exolab.castor.types.Date date = new org.exolab.castor.types.Date( + new java.util.Date()); + Entry provEntry; + + if (jprov != null) + { + entries = jprov.getEntries(); + for (int i = 0; i < entries.length; i++) + { + provEntry = new Entry(); + try + { + date = new org.exolab.castor.types.Date(entries[i].getDate()); + } catch (Exception ex) + { + ex.printStackTrace(); + + date = new org.exolab.castor.types.Date(entries[i].getDate()); + } + provEntry.setDate(date); + provEntry.setUser(entries[i].getUser()); + provEntry.setAction(entries[i].getAction()); + prov.addEntry(provEntry); + } + } + else + { + provEntry = new Entry(); + provEntry.setDate(date); + provEntry.setUser(System.getProperty("user.name")); // TODO: ext string + provEntry.setApp("JVAPP"); // TODO: ext string + provEntry.setAction(action); + prov.addEntry(provEntry); + } + + return prov; + } + */ + jalview.datamodel.Provenance getJalviewProvenance(Provenance prov) + { + // TODO: fix App and Action entries and check use of provenance in jalview. + jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance(); + for (int i = 0; i < prov.getEntryCount(); i++) + { + jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i).getAction(), + prov.getEntry(i).getDate().toDate(), + prov.getEntry(i).getId()); + } + + return jprov; + } + + /** + * + * @return default initial provenance list for a Jalview created vamsas + * object. + */ + Provenance dummyProvenance() + { + return dummyProvenance(null); + } + + Entry dummyPEntry(String action) + { + Entry entry = new Entry(); + entry.setApp(this.provEntry.getApp()); + if (action != null) + { + entry.setAction(action); + } + else + { + entry.setAction("created."); + } + entry.setDate(new org.exolab.castor.types.Date(new java.util.Date())); + entry.setUser(this.provEntry.getUser()); + return entry; + } + + Provenance dummyProvenance(String action) + { + Provenance prov = new Provenance(); + prov.addEntry(dummyPEntry(action)); + return prov; + } + + void addProvenance(Provenance p, String action) + { + p.addEntry(dummyPEntry(action)); + } + +}